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1 #
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2 # Ensembl module for Bio::EnsEMBL::Funcgen::ExperimentalSubset
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3 #
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4 # You may distribute this module under the same terms as Perl itself
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5
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6 =head1 NAME
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7
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8 Bio::EnsEMBL::ExperimentalSet - A module to represent ExperimentalSubset object.
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9
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10
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11 =head1 SYNOPSIS
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12
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13 use Bio::EnsEMBL::Funcgen::ExperimetnalSubset;
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14
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15 my $data_set = Bio::EnsEMBL::Funcgen::ExperimentalSubset->new(
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16 -DBID => $dbID,
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17 -ADAPTOR => $self,
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18 -NAME => $name,
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19 -EXPERIMENTAL_SET => $eset,
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20 );
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21
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22
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23
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24 =head1 DESCRIPTION
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25
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26 An ExperimentalSubset object is a very simple skeleton class to enable storage of associated subset states. As such there
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27 are only very simple accessor methods for basic information, and there is no namesake adaptor, rather is is handled by the
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28 ExperimentalSetAdaptor.
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29
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30 =head1 AUTHOR
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31
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32 This module was created by Nathan Johnson.
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33
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34 This module is part of the Ensembl project: http://www.ensembl.org/
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35
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36 =head1 CONTACT
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37
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38 Post comments or questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
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39
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40 =head1 METHODS
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41
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42 =cut
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43
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44 use strict;
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45 use warnings;
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46
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47 package Bio::EnsEMBL::Funcgen::ExperimentalSubset;
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48
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49 use Bio::EnsEMBL::Utils::Argument qw( rearrange );
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50 use Bio::EnsEMBL::Utils::Exception qw( throw );
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51 use Bio::EnsEMBL::Funcgen::Storable;
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52
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53 use vars qw(@ISA);
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54 @ISA = qw(Bio::EnsEMBL::Funcgen::Storable);
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55
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56
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57 =head2 new
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58
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59 Example : my $eset = Bio::EnsEMBL::Funcgen::ExperimentalSubset->new(
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60 -DBID => $dbID,
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61 -ADAPTOR => $self,
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62 -NAME => $name,
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63 -EXPERIMENTAL_SET => $eset,
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64 );
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65
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66
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67 Description: Constructor for ExperimentalSubset objects.
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68 Returntype : Bio::EnsEMBL::Funcgen::ExperimentalSubset
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69 Exceptions : Throws if no name defined
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70 Throws if CellType or FeatureType are not valid or stored
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71 Caller : General
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72 Status : At risk
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73
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74 =cut
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75
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76 sub new {
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77 my $caller = shift;
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78
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79 my $class = ref($caller) || $caller;
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80
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81 my $self = $class->SUPER::new(@_);
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82
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83 #do we need to add $fg_ids to this? Currently maintaining one feature_group focus.(combi exps?)
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84 my ($name, $eset)
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85 = rearrange(['NAME', 'EXPERIMENTAL_SET'], @_);
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86
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87
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88 throw('Must provide a name argument') if ! defined $name;
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89
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90 if(!(ref($eset) &&
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91 $eset->isa('Bio::EnsEMBL::Funcgen::ExperimentalSet')
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92 && $eset->dbID())){
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93 throw('Must provide a valid stored experimental_set argument');
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94 }
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95
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96
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97 $self->{'name'} = $name;
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98 $self->{'experimental_set'} = $eset;
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99
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100 return $self;
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101 }
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102
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103
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104 =head2 name
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105
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106 Example : my $name = $exp_sset->name();
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107 Description: Getter for the name of this ExperimentalSubset.
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108 Returntype : string
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109 Exceptions : None
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110 Caller : General
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111 Status : At Risk
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112
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113 =cut
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114
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115 sub name {
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116 my $self = shift;
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117 return $self->{'name'};
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118 }
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119
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120 =head2 experimental_set
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121
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122 Example : my $eset = $exp_sset->experimental_set();
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123 Description: Getter for the experimental_set attribute of this ExperimentalSubset.
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124 Returntype : Bio::EnsEMBL::Funcgen::ExperimentalSet
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125 Exceptions : None
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126 Caller : General
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127 Status : At Risk
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128
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129 =cut
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130
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131 sub experimental_set {
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132 my $self = shift;
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133 return $self->{'experimental_set'};
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134 }
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135
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136
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137
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138 1;
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139
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